› 4dj4

X-ray diffraction
2.35Å resolution

X-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)

Released:
DOI: 10.2210/pdb4dj4/pdb
PDB entry 4dj4 coloured by chain, front view.
PDB entry 4dj4 coloured by chain, side view.
PDB entry 4dj4 coloured by chain, top view.
Source organism: Solanum lycopersicum
Primary publication:
Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.
Koval' T, Lipovová P, Podzimek T, Matoušek J, Dušková J, Skálová T, Stěpánková A, Hašek J, Dohnálek J
Acta Crystallogr D Biol Crystallogr 69 213-26 (2013)
PMID: 23385457

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170984 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Aspergillus nuclease S1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 277 amino acids
Theoretical weight: 31.65 KDa
Source organism: Solanum lycopersicum
Expression system: Nicotiana benthamiana
UniProt:
  • Canonical: Q0KFV0 (Residues: 26-302; Coverage: 100%)
Gene name: tbn1
Sequence domains: S1/P1 Nuclease
Structure domains: P1 Nuclease

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand ZN 6 x ZN
Ligand CL 2 x CL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: R3
Unit cell:
a: 113.322Å b: 113.322Å c: 138.322Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.183 0.207
Expression system: Nicotiana benthamiana

Quick links

Citations

3 citation in other articles

Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.
Yu et al. (2014)
2 more

1 mention without citation

Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme.
Stránský et al. (2015)